[gmx-users] Add additional LJ to certain atom pair- experience and a funny result

[jia jia]

Dear Mark:
    Thank you for your reply! However, I just solve the problem....it
origins from another reason.
    I've check source code, the 1-4 interaction is exampt from cutoff or
shit function---they are always calculted no matter how far the two atom.
As a result, when the two atom move away and pass the cutoff distance, the
simulation use LJ potentional drift from the simulation use 1-4 interaction.
    When a large cutoff used, the two simulation give identical result  :)


Cheers
Guang





2014-02-21 16:34 GMT-06:00 Mark Abraham <mark.j.abraham at gmail.com>:

> If you want a reproducible trajectory, you should consider the thoughts
> here http://www.gromacs.org/Documentation/Terminology/Reproducibility
>
> Mark
>
>
> On Fri, Feb 21, 2014 at 6:23 PM, jia jia <jzg579 at gmail.com> wrote:
>
> > Dear all:
> >    I'm trying to add additional LJ potential to certain atom pair, e.g.
> for
> > atom 1 and 2, except normal atom LJ and Coulomb depend on atom type, I
> want
> > add an additional LJ to them (so, only for atom 1 and 2, they will have
> > Vorin+Vadd). I'm using gromcas 4.0.5 (double precision).
> >    My way to do this is add a line for " 1 2 1 C6value C12value" to the
> > paires as the gromacs does no scale 1-4 potential.
> >    To test whether it work, I've set a system contain only two non-bonded
> > atom, then perform two 1-cpu, 40 step simulation (output v, f every
> step),
> > one simulation is with origin LJ potential, one simulation is add the
> line
> > " 1 2 1 C6value C12value" to paires, and change the C6 C12 value of atom
> 1
> > 2 in XXnb.itp (or other nonbond parameter file) to "0 0".
> >    With this change, I'm expecting the two simulation give identical
> > result.
> >
> >    I've checked the result with gmxdump, when using G53a6, yes, after 40
> > step two siimulations give identical results.
> >
> >    However, when use Martini, the 0 - 10 step is identical, after that
> > there is growing difference between them. At the end of 40steps, the
> > difference in coordinations is about 0.0002 nm, and for the force is also
> > about 0.0002.
> >    If I run a simulation from a second time, the result from second run
> is
> > indentical with  previous run. This suggest the differences are not from
> > machine  error.
> >
> >    Has any one test this before or have any idea where this error from?
> >
> >    I doubt the error may from define variable, e.g. the progrom treat LJ
> > and 1-4 interaction in different precision.
> >    I'll contine test and check source, If I find anything I'll report
> here.
> >
> > Cheers
> > Guang
> > --
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